fix: remove pytest/xfail test marks

Author: oesteban

nitransforms/io/fsl.py

@@ -68,7 +68,6 @@ def from_string(cls, string):
         if not lines or len(lines) < 4:
             raise TransformFileError
 
-        print(lines)
         sa["parameters"] = np.genfromtxt(
             ["\n".join(lines)], dtype=cls.dtype["parameters"]
         )

nitransforms/tests/test_io.py

@@ -165,7 +165,6 @@ def test_LT_conversions(data_path, fname):
     assert np.allclose(r2r_m, v2v_m, rtol=1e-04)
 
 
-@pytest.mark.xfail(raises=(FileNotFoundError, NotImplementedError))
 @pytest.mark.parametrize(
     "image_orientation",
     [
@@ -177,6 +176,9 @@ def test_LT_conversions(data_path, fname):
 )
 @pytest.mark.parametrize("sw", ["afni", "fsl", "fs", "itk"])
 def test_Linear_common(tmpdir, data_path, sw, image_orientation, get_testdata):
+    if (image_orientation, sw) == ("oblique", "afni"):
+        pytest.skip("AFNI Deoblique unsupported.")
+
     tmpdir.chdir()
 
     moving = get_testdata[image_orientation]

nitransforms/tests/test_linear.py

@@ -139,11 +139,13 @@ def test_loadsave(tmp_path, data_path, testdata_path, fmt):
         assert xfm == nitl.load(fname, fmt=fmt, reference=ref_file)
 
 
-@pytest.mark.xfail(reason="Not fully implemented")
 @pytest.mark.parametrize("image_orientation", ["RAS", "LAS", "LPS", "oblique"])
 @pytest.mark.parametrize("sw_tool", ["itk", "fsl", "afni", "fs"])
 def test_linear_save(tmpdir, data_path, get_testdata, image_orientation, sw_tool):
     """Check implementation of exporting affines to formats."""
+    if (image_orientation, sw_tool) == ("oblique", "afni"):
+        pytest.skip("AFNI Deoblique unsupported.")
+
     tmpdir.chdir()
     img = get_testdata[image_orientation]
     # Generate test transform

nitransforms/tests/test_nonlinear.py

@@ -49,12 +49,13 @@ def test_itk_disp_load_intent():
     assert field.header.get_intent()[0] == "vector"
 
 
-@pytest.mark.xfail(reason="Oblique datasets not fully implemented")
 @pytest.mark.parametrize("image_orientation", ["RAS", "LAS", "LPS", "oblique"])
 @pytest.mark.parametrize("sw_tool", ["itk", "afni"])
 @pytest.mark.parametrize("axis", [0, 1, 2, (0, 1), (1, 2), (0, 1, 2)])
 def test_displacements_field1(tmp_path, get_testdata, image_orientation, sw_tool, axis):
     """Check a translation-only field on one or more axes, different image orientations."""
+    if (image_orientation, sw_tool) == ("oblique", "afni") and axis in ((1, 2), (0, 1, 2)):
+        pytest.skip("AFNI Deoblique unsupported.")
     os.chdir(str(tmp_path))
     nii = get_testdata[image_orientation]
     nii.to_filename("reference.nii.gz")